Re: CGMD parameters

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Wed Dec 24 2008 - 07:27:25 CST

Hi Bin,
the virus trajectories were chosen simply because they represented the
largest body of data we had available to get reasonable average
parameters for the bonded interactions. We did, of course, check their
reasonability by comparing to other simulations, and they should not be
specific to any one case (the primary application of the model has been
to HDL particles, and has in general been quite successful). However, if
you feel the need to change them to reflect some other simulation data,
you shouldn't be any worse off so long as you have enough data on each
amino acid in a variety of environments.

With that said, martini in namd is still coming, and will probably be a
better option in the near future, given that martini is a better general
purpose protein forcefield on this scale.

Best,
Peter

BIN ZHANG wrote:
> Dear All:
>
> I had a question about the parameters in rbcg-2007.par.
>
> Can I change the equilibrium values of bonds, angles, and dihedrals
> (of protein) in there as I wish without modifying the non bonded
> interaction parameters? In other words, are these parameters optimized
> together with those for non bonded interaction to reproduce some AA
> simulation results?
>
> I checked the paper (Coarse grained protein-lipid model with
> application to lipoprotein particles. Amy Y. Shih, Anton Arkhipov,
> Peter L. Freddolino, and Klaus Schulten. Journal of Physical Chemistry
> B, 110:3674-3684, 2006), where it says, the bonds, angles are taken
> from the equilibrium value(EV) of a virus structure. Is it still the
> case here? If so, I would naively guess that it should be safe to
> change these parameters to EV of other proteins.
>
> Thanks in advance.
>
> Bin
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> -------------------------------------------------------------
> The tree of liberty must be refreshed from time to time with the blood
> of patriots and tyrants.

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